3Q96

B-Raf kinase domain in complex with a tetrahydronaphthalene inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design and optimization of potent and orally bioavailable tetrahydronaphthalene raf inhibitors.

Gould, A.E.Adams, R.Adhikari, S.Aertgeerts, K.Afroze, R.Blackburn, C.Calderwood, E.F.Chau, R.Chouitar, J.Duffey, M.O.England, D.B.Farrer, C.Forsyth, N.Garcia, K.Gaulin, J.Greenspan, P.D.Guo, R.Harrison, S.J.Huang, S.C.Iartchouk, N.Janowick, D.Kim, M.S.Kulkarni, B.Langston, S.P.Liu, J.X.Ma, L.T.Menon, S.Mizutani, H.Paske, E.Renou, C.C.Rezaei, M.Rowland, R.S.Sintchak, M.D.Smith, M.D.Stroud, S.G.Tregay, M.Tian, Y.Veiby, O.P.Vos, T.J.Vyskocil, S.Williams, J.Xu, T.Yang, J.J.Yano, J.Zeng, H.Zhang, D.M.Zhang, Q.Galvin, K.M.

(2011) J.Med.Chem. 54: 1836-1846

  • DOI: 10.1021/jm101479y

  • PubMed Abstract: 
  • Inhibition of mutant B-Raf signaling, through either direct inhibition of the enzyme or inhibition of MEK, the direct substrate of Raf, has been demonstrated preclinically to inhibit tumor growth. Very recently, treatment of B-Raf mutant melanoma pat ...

    Inhibition of mutant B-Raf signaling, through either direct inhibition of the enzyme or inhibition of MEK, the direct substrate of Raf, has been demonstrated preclinically to inhibit tumor growth. Very recently, treatment of B-Raf mutant melanoma patients with a selective B-Raf inhibitor has resulted in promising preliminary evidence of antitumor activity. This article describes the design and optimization of tetrahydronaphthalene-derived compounds as potent inhibitors of the Raf pathway in vitro and in vivo. These compounds possess good pharmacokinetic properties in rodents and inhibit B-Raf mutant tumor growth in mouse xenograft models.


    Organizational Affiliation

    Millennium Pharmaceuticals, Inc., 40 Landsdowne Street, Cambridge, Massachusetts 02139, United States. sandy.gould@mpi.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
282Homo sapiensMutation(s): 0 
Gene Names: BRAF (BRAF1, RAFB1)
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to Gene View: BRAF
Go to UniProtKB:  P15056
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0NF
Query on 0NF

Download SDF File 
Download CCD File 
A, B
(2S)-N-[3-(2-aminopropan-2-yl)-5-(trifluoromethyl)phenyl]-7-[(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-4-yl)oxy]-1,2,3,4-tetrahydronaphthalene-2-carboxamide
C29 H29 F3 N4 O3
NHVJQLRLGGPUJY-KRWDZBQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0NFIC50: 2.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.029α = 90.00
b = 94.029β = 90.00
c = 165.264γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description